Recombinomics
Commentary 07:36
May 19, 2008Sequences from two of the
whooper swan isolates from Hokkaido have been made public. Satoko
Onishi and colleagues at Hokkaido University are to be commended on the
prompt release of the sequences. Full sequences from all eight
gene segments have been released for one isolate, A/whooper
swan/Hokkaido/1/2008, and partial sequences released for the other,
A/whooper
swan/Hokkaido/2/2008.
Both sets of sequences are closely related to each other.

The HA sequences are most closely to clade 2.3.2 sequences from
Vietnam, but they have a large number of non synonymous changes,
including M230I. M230I is a receptor binding domain change found
in the Gharbiya
cluster and many more recent poultry isolates in Egypt. It is
also found in seasonal flu (H1N1, H3N2, influenza
B), and is linked to fatal cases in Egypt. It is likely that
M230I is also in isolates in South Korea, including the H5N1 that
infected the soldier. Although he did recover, he developed
pneumonia and lost consciousness. The sequences from Japan also
had polymorphisms that are almost exclusively in clade 2.2 isolates
(see list here
and here).

Although the HA sequences are most closely related to clade 2.3.2, the
other gene segments are closely related to clade 2.3.4, including human
isolates such as A/human/China/GD02/2006.
These relationships suggest there have been considerable exchanges of
genetic information via recombination and reassortment. The PB2
sequence also has a region that matches sequences from North America,
raising additional concerns that the migratory birds in northern Japan
migrate into North America. The acquisitions signal additional
global expansion by clade 2.3 and remain cause for concern.